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https://github.com/pepijn-devries/ECOTOXr

R package that creates a local SQLite build of (and allows querying of) the US EPA ECOTOX database.
https://github.com/pepijn-devries/ECOTOXr

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R package that creates a local SQLite build of (and allows querying of) the US EPA ECOTOX database.

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README 

        
---

output: github_document

---



```{r, echo = FALSE, message = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-"

)

library(ECOTOXr)

```



# `ECOTOXr`

> Harness information from the [US EPA ECOTOXicology Knowledgebase](https://cfpub.epa.gov/ecotox/)



[![R build status](https://github.com/pepijn-devries/ECOTOXr/workflows/R-CMD-check/badge.svg)](https://github.com/pepijn-devries/ECOTOXr/actions)

[![version](https://www.r-pkg.org/badges/version/ECOTOXr)](https://CRAN.R-project.org/package=ECOTOXr)

![cranlogs](https://cranlogs.r-pkg.org/badges/ECOTOXr)



## Overview



ECOTOXr logo

`ECOTOXr` can be used to explore and analyse data from the [US EPA ECOTOX database](https://cfpub.epa.gov/ecotox/).

More specifically you can:



 * Build a local SQLite copy of the [US EPA ECOTOX database](https://cfpub.epa.gov/ecotox/)

 * Search and extract data from the local database

 * Use experimental features to search the on-line dashboards: [ECOTOX](https://cfpub.epa.gov/ecotox/search.cfm) and

   [CompTox](https://comptox.epa.gov/dashboard/batch-search)



## Why use `ECOTOXr`?



The `ECOTOXr` package allows you to search and extract data from the [ECOTOXicological Knowledgebase](https://cfpub.epa.gov/ecotox/)

and import it directly into `R`. This will allow you to formalize and document the search- and extract-procedures in `R` code.

This makes it easier to share and reproduce such procedures and its results. Moreover, you can directly apply any statistical

analysis offered in `R`.



## Installation 



> Get CRAN version

```{r eval=FALSE}

install.packages("ECOTOXr")

```



> Get development version from r-universe

```{r eval=FALSE}

install.packages("ECOTOXr", repos = c("https://pepijn-devries.r-universe.dev", "https://cloud.r-project.org"))

```



## Usage



### Preparing the database



Although `ECOTOXr` has experimental features to search the on-line database. The package will

reach its full potential when you build a copy of the database on your local machine.



> Download and build a local copy of the latest ASCII export of the US EPA ECOTOX database



```{r eval=FALSE}

download_ecotox_data()

```



### Searching the local database for species and substances



Obviously, searching the local database is only possible after the download and build is

ready (see previous section).



> Search the local database for tests of water flea Daphnia magna exposed to benzene



```{r eval=FALSE}

search_ecotox(

  list(

    latin_name    = list(terms = "Daphnia magna", method = "exact"),

    chemical_name = list(terms = "benzene",       method = "exact")

  )

)

```



### Three ways of querying the local database



Let's have a look at 3 different approaches for retrieving a specific record from the local database, using the

unique identifier `result_id`. The first option is to use the build in `search_ecotox` function. It uses

simple `R` syntax and allows you to search and collect any field from any table in the database. Furthermore,

all requested output fields are automatically joined to the result without the end-user needing to know anything

about the database structure.



> Using the prefab function `search_ecotox` packaged by `ECOTOXr`



```{r warning = FALSE}

search_ecotox(

  list(

    result_id = list(terms = "401386", method = "exact")

  ),

  as_data_frame = F

)

```



If you like to use [`dplyr`](https://dplyr.tidyverse.org/) verbs, you are in luck. SQLite database can be approached using

`dplyr` verbs. This approach will only return information from the `results` table. The end-user will have to join other information

(like test species and test substance) manually. This does require knowledge of the database structure.



> Using `dplyr` verbs



```{r warning = FALSE}

con <- dbConnectEcotox()

dplyr::tbl(con, "results") |>

  dplyr::filter(result_id == "401386") |>

  dplyr::collect()

```



If you prefer working using `SQL` directly, that is fine too. The [`RSQLite`](https://cran.r-project.org/package=RSQLite) package

allows you to get queries using `SQL` statements. The result is identical to that of the previous approach. Here too the end-user

needs knowledge of the database structure in order to join additional data.



> Using `SQL` syntax



```{r warning = FALSE}

dbGetQuery(con, "SELECT * FROM results WHERE result_id='401386'") |>

  dplyr::as_tibble()

```



## Disclaimers



It is the end-users own responsibility to check the quality of collected data, using the original referenced source in order to evaluate its

fitness for use, see also: .



Note that the package maintainer is not affiliated with the US EPA, this package is therefore **not** official US EPA software.



## Resources



 * De Vries, P. (2024) ECOTOXr: An R package for reproducible and transparent retrieval of data from EPA's ECOTOX database. _Chemosphere_ 364 143078 

 * [Manual of the CRAN release](https://CRAN.R-project.org/package=ECOTOXr)

 * EPA ECOTOX help 

 * Olker, Jennifer H.; Elonen, Colleen M.; Pilli, Anne; Anderson, Arne; Kinziger, Brian; Erickson, Stephen; Skopinski, Michael;

   Pomplun, Anita; LaLone, Carlie A.; Russom, Christine L.; Hoff, Dale. (2022): The ECOTOXicology Knowledgebase: A Curated Database of

   Ecologically Relevant Toxicity Tests to Support Environmental Research and Risk Assessment. _Environmental Toxicology and Chemistry_

   41(6) 1520-1539